Working with men and boys is central to improving sexual and reproductive health and rights and contributes to gender equality and social justice. Focusing on two behaviour change interventions (“One Youth Can” and “SKILLZ Guyz”), embedded within a national HIV programme (“My Journey”), this qualitative, exploratory study explored the contextual and organizational realities faced by peer facilitators in implementing these two interventions and what it would take to integrate a gender-transformative approach into their practice. The research, conducted in South Africa, used three data sources: a curriculum gender analysis, observations of both interventions and capacity strengthening sessions with peer facilitators. The study found that facilitators have to manage an array of contextual challenges. The programmatic context in which they work is dominated by the need to meet quantitative targets, leaving the capacity strengthening and mentoring needs of the facilitators – and their own lived experiences insufficiently addressed. Our research confirms the pivotal role peer facilitators can play in implementing gender-transformative approaches with adolescent boys and men in South Africa, but recommends that their practice be accompanied by sustained capacity strengthening and organisational support to address the unequal systems of gender and intersecting power relations in the contexts in which they work and live.